simple	04-Mar-2026 12:01:23	Build Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #5 (JB-GDB744-JOB1-5) started building on agent Default Agent
simple	04-Mar-2026 12:01:23	
simple	04-Mar-2026 12:01:23	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1
simple	04-Mar-2026 12:01:23	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #5 (JB-GDB744-JOB1-5)
simple	04-Mar-2026 12:01:23	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	04-Mar-2026 12:01:23	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1
simple	04-Mar-2026 12:01:23	Updating source code to revision: c36b1d121eaf5e74db628f810d4ee72164870015
simple	04-Mar-2026 12:01:23	Fetching 'refs/heads/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	04-Mar-2026 12:01:23	Checking out revision c36b1d121eaf5e74db628f810d4ee72164870015.
simple	04-Mar-2026 12:01:23	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	04-Mar-2026 12:01:23	   944aa49..c36b1d1  bug/JAL-4624_JAL-4623_Mul_SS_in_PCA -> origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA
simple	04-Mar-2026 12:01:23	 * [new branch]      epic/JAL-4320_JAL-4644_refactor_directory_structure -> origin/epic/JAL-4320_JAL-4644_refactor_directory_structure
simple	04-Mar-2026 12:01:23	   9efd725..b443e47  epic/JAL-4320_gradle_upgrade_to_gradle9 -> origin/epic/JAL-4320_gradle_upgrade_to_gradle9
simple	04-Mar-2026 12:01:24	Already on 'bug/JAL-4624_JAL-4623_Mul_SS_in_PCA'
simple	04-Mar-2026 12:01:24	Your branch is behind 'origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' by 1 commit, and can be fast-forwarded.
simple	04-Mar-2026 12:01:24	  (use "git pull" to update your local branch)
simple	04-Mar-2026 12:01:24	HEAD is now at c36b1d1 JAL-4623 Changes for labels in output points file
simple	04-Mar-2026 12:01:24	Updated source code to revision: c36b1d121eaf5e74db628f810d4ee72164870015
simple	04-Mar-2026 12:01:24	Finished task 'Checkout Default Repository' with result: Success
simple	04-Mar-2026 12:01:24	Running pre-build action: VCS Version Collector
simple	04-Mar-2026 12:01:24	Running pre-build action: Artifactory Release Staging
simple	04-Mar-2026 12:01:24	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	04-Mar-2026 12:01:24	Bamboo Artifactory Plugin version: 2.6.2
command	04-Mar-2026 12:01:24	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #5 (JB-GDB744-JOB1-5)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-5\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB744-JOB1\nbamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=5\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-5\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_shortPlanKey=GDB744\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_buildTimeStamp=2026-03-04T12:01:23.259Z\nbamboo_repository_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDB744-JOB1-5\nbamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests\nbamboo_repository_48169013_git_username=\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_48169013_name=Jalview Gitlab\nbamboo_planRepository_1_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169013_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_48169013_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_48169013_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_48169013_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972457\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169013_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1\nbamboo_planKey=JB-GDB744\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	04-Mar-2026 12:01:24	2414
build	04-Mar-2026 12:01:30	
build	04-Mar-2026 12:01:30	> Configure project :
build	04-Mar-2026 12:01:30	Using properties from file './utils/channels/default/channel_gradle.properties'
build	04-Mar-2026 12:01:30	JALVIEW_VERSION is set to '2.12.0'
build	04-Mar-2026 12:01:30	HEADLESS BUILD
build	04-Mar-2026 12:01:30	J2S ENABLED
build	04-Mar-2026 12:01:30	Using a LOCAL profile.
build	04-Mar-2026 12:01:31	eclipseDir exists
build	04-Mar-2026 12:01:32	
build	04-Mar-2026 12:01:32	> Task :clean
build	04-Mar-2026 12:01:32	> Task :cleanClover
build	04-Mar-2026 12:01:32	> Task :cleanTest UP-TO-DATE
build	04-Mar-2026 12:01:34	
build	04-Mar-2026 12:01:34	> Task :cloverInstrJava
build	04-Mar-2026 12:01:34	Clover: About to instrument 1255 files
build	04-Mar-2026 12:01:34	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Mar-2026 12:01:34	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover.db'.
build	04-Mar-2026 12:01:34	Processing files at 1.9 source level.
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Mar-2026 12:01:38	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
build	04-Mar-2026 12:01:43	Clover all over. Instrumented 1255 files (133 packages).
build	04-Mar-2026 12:01:45	
build	04-Mar-2026 12:01:45	> Task :cloverInstrTests
build	04-Mar-2026 12:01:45	Clover: About to instrument test files
build	04-Mar-2026 12:01:45	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Mar-2026 12:01:45	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover.db'.
build	04-Mar-2026 12:01:45	Processing files at 1.9 source level.
build	04-Mar-2026 12:01:48	Clover all over. Instrumented 315 files (58 packages).
build	04-Mar-2026 12:01:48	1771 test methods detected.
build	04-Mar-2026 12:01:48	
build	04-Mar-2026 12:01:48	> Task :cloverInstr
build	04-Mar-2026 12:01:50	
build	04-Mar-2026 12:01:50	> Task :compileCloverJava
build	04-Mar-2026 12:01:50	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	04-Mar-2026 12:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:01:50	Setting target compatibility to 11
error	04-Mar-2026 12:02:12	Note: Some input files use or override a deprecated API.
error	04-Mar-2026 12:02:12	Note: Recompile with -Xlint:deprecation for details.
error	04-Mar-2026 12:02:12	Note: Some input files use unchecked or unsafe operations.
error	04-Mar-2026 12:02:12	Note: Recompile with -Xlint:unchecked for details.
build	04-Mar-2026 12:02:19	
build	04-Mar-2026 12:02:19	> Task :processCloverResources NO-SOURCE
build	04-Mar-2026 12:02:19	> Task :cloverClasses
build	04-Mar-2026 12:02:20	> Task :copyHelp
build	04-Mar-2026 12:02:21	> Task :buildIndices
build	04-Mar-2026 12:02:21	> Task :copyResources
build	04-Mar-2026 12:02:21	> Task :copyChannelResources
build	04-Mar-2026 12:02:21	
build	04-Mar-2026 12:02:21	> Task :createBuildProperties
build	04-Mar-2026 12:02:21	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	04-Mar-2026 12:02:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:21	
build	04-Mar-2026 12:02:21	> Task :buildResources
build	04-Mar-2026 12:02:21	> Task :copyDocs
build	04-Mar-2026 12:02:21	
build	04-Mar-2026 12:02:21	> Task :convertMdFiles
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/building.html
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	04-Mar-2026 12:02:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	04-Mar-2026 12:02:22	
build	04-Mar-2026 12:02:22	> Task :releasesTemplates
build	04-Mar-2026 12:02:22	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	04-Mar-2026 12:02:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:22	Stripping rc/test/etc for TEST
build	04-Mar-2026 12:02:22	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	04-Mar-2026 12:02:22	
build	04-Mar-2026 12:02:22	> Task :prepare
build	04-Mar-2026 12:02:24	
build	04-Mar-2026 12:02:24	> Task :compileJava
build	04-Mar-2026 12:02:24	Setting target compatibility to 11
error	04-Mar-2026 12:02:30	Note: Some input files use or override a deprecated API.
error	04-Mar-2026 12:02:30	Note: Recompile with -Xlint:deprecation for details.
error	04-Mar-2026 12:02:30	Note: Some input files use unchecked or unsafe operations.
error	04-Mar-2026 12:02:30	Note: Recompile with -Xlint:unchecked for details.
build	04-Mar-2026 12:02:34	
build	04-Mar-2026 12:02:34	> Task :compileTestJava
build	04-Mar-2026 12:02:34	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	04-Mar-2026 12:02:34	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes'. Reason: Task ':compileTestJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:34	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-test-instr'. Reason: Task ':compileTestJava' uses this output of task ':cloverInstrTests' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:34	Setting target compatibility to 11
error	04-Mar-2026 12:02:41	Note: Some input files use or override a deprecated API.
error	04-Mar-2026 12:02:41	Note: Recompile with -Xlint:deprecation for details.
error	04-Mar-2026 12:02:41	Note: Some input files use unchecked or unsafe operations.
error	04-Mar-2026 12:02:41	Note: Recompile with -Xlint:unchecked for details.
build	04-Mar-2026 12:02:42	
build	04-Mar-2026 12:02:42	> Task :processTestResources
build	04-Mar-2026 12:02:42	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	04-Mar-2026 12:02:42	
build	04-Mar-2026 12:02:42	> Task :testClasses
build	04-Mar-2026 12:02:44	
build	04-Mar-2026 12:02:44	> Task :testTask0
build	04-Mar-2026 12:02:44	Running tests WITH clover
error	04-Mar-2026 12:02:46	WARNING: An illegal reflective access operation has occurred
error	04-Mar-2026 12:02:46	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Mar-2026 12:02:46	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Mar-2026 12:02:46	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Mar-2026 12:02:46	WARNING: All illegal access operations will be denied in a future release
build	04-Mar-2026 12:07:35	
build	04-Mar-2026 12:07:35	> Task :testTask1
build	04-Mar-2026 12:07:35	Running tests WITH clover
error	04-Mar-2026 12:07:36	WARNING: An illegal reflective access operation has occurred
error	04-Mar-2026 12:07:36	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Mar-2026 12:07:36	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Mar-2026 12:07:36	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Mar-2026 12:07:36	WARNING: All illegal access operations will be denied in a future release
build	04-Mar-2026 12:09:42	
build	04-Mar-2026 12:09:42	> Task :testTask2
build	04-Mar-2026 12:09:42	Running tests WITH clover
error	04-Mar-2026 12:09:43	WARNING: An illegal reflective access operation has occurred
error	04-Mar-2026 12:09:43	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Mar-2026 12:09:43	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Mar-2026 12:09:43	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Mar-2026 12:09:43	WARNING: All illegal access operations will be denied in a future release
build	04-Mar-2026 12:09:47	
build	04-Mar-2026 12:09:47	> Task :testTask3
build	04-Mar-2026 12:09:47	Running tests WITH clover
error	04-Mar-2026 12:09:49	WARNING: An illegal reflective access operation has occurred
error	04-Mar-2026 12:09:49	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Mar-2026 12:09:49	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Mar-2026 12:09:49	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Mar-2026 12:09:49	WARNING: All illegal access operations will be denied in a future release
build	04-Mar-2026 12:10:06	
build	04-Mar-2026 12:10:06	> Task :test NO-SOURCE
build	04-Mar-2026 12:10:06	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	04-Mar-2026 12:10:06	│jalview:testTask0 results: SUCCESS (2104 tests, 2104 successes, 0 failures, 0 skipped) in 4 minutes, 49.147 seconds   │
build	04-Mar-2026 12:10:06	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask0/index.html│
build	04-Mar-2026 12:10:06	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Mar-2026 12:10:06	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 7.053 seconds        │
build	04-Mar-2026 12:10:06	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask1/index.html│
build	04-Mar-2026 12:10:06	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Mar-2026 12:10:06	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.416 seconds                     │
build	04-Mar-2026 12:10:06	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask2/index.html│
build	04-Mar-2026 12:10:06	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Mar-2026 12:10:06	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.969 seconds                  │
build	04-Mar-2026 12:10:06	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask3/index.html│
build	04-Mar-2026 12:10:06	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Mar-2026 12:10:06	│OVERALL: results: SUCCESS (2181 tests, 2180 successes, 0 failures, 1 skipped) in 6 minutes, 82.585 seconds            │
build	04-Mar-2026 12:10:06	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	04-Mar-2026 12:10:06	
build	04-Mar-2026 12:10:06	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	04-Mar-2026 12:10:06	
build	04-Mar-2026 12:10:06	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	04-Mar-2026 12:10:06	
build	04-Mar-2026 12:10:06	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	04-Mar-2026 12:10:06	
build	04-Mar-2026 12:10:06	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	04-Mar-2026 12:10:06	Please consult deprecation warnings for more details.
build	04-Mar-2026 12:10:06	
build	04-Mar-2026 12:10:06	BUILD SUCCESSFUL in 8m 42s
build	04-Mar-2026 12:10:06	21 actionable tasks: 20 executed, 1 up-to-date
simple	04-Mar-2026 12:10:07	Finished task 'Run tests with openclover under gradle' with result: Success
simple	04-Mar-2026 12:10:07	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	04-Mar-2026 12:10:07	Bamboo Artifactory Plugin version: 2.6.2
command	04-Mar-2026 12:10:07	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #5 (JB-GDB744-JOB1-5)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-5\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB744-JOB1\nbamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=5\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-5\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_shortPlanKey=GDB744\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_buildTimeStamp=2026-03-04T12:01:23.259Z\nbamboo_repository_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDB744-JOB1-5\nbamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests\nbamboo_repository_48169013_git_username=\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_48169013_name=Jalview Gitlab\nbamboo_planRepository_1_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169013_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_48169013_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_48169013_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_48169013_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972457\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169013_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1\nbamboo_planKey=JB-GDB744\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	04-Mar-2026 12:10:07	2414
build	04-Mar-2026 12:10:13	
build	04-Mar-2026 12:10:13	> Configure project :
build	04-Mar-2026 12:10:13	Using properties from file './utils/channels/default/channel_gradle.properties'
build	04-Mar-2026 12:10:13	JALVIEW_VERSION is set to '2.12.0'
build	04-Mar-2026 12:10:13	HEADLESS BUILD
build	04-Mar-2026 12:10:13	J2S ENABLED
build	04-Mar-2026 12:10:13	Using a LOCAL profile.
build	04-Mar-2026 12:10:14	eclipseDir exists
build	04-Mar-2026 12:10:16	
build	04-Mar-2026 12:10:16	> Task :cloverHtmlReport
build	04-Mar-2026 12:10:16	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Mar-2026 12:10:17	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/clover'
build	04-Mar-2026 12:11:10	Done. Processed 137 packages in 52529ms (383ms per package).
build	04-Mar-2026 12:11:15	
build	04-Mar-2026 12:11:15	> Task :cloverXmlReport
build	04-Mar-2026 12:11:15	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Mar-2026 12:11:16	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/clover/clover.xml'
build	04-Mar-2026 12:11:17	
build	04-Mar-2026 12:11:17	> Task :cloverReport
build	04-Mar-2026 12:11:17	
build	04-Mar-2026 12:11:17	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	04-Mar-2026 12:11:17	
build	04-Mar-2026 12:11:17	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	04-Mar-2026 12:11:17	
build	04-Mar-2026 12:11:17	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	04-Mar-2026 12:11:17	
build	04-Mar-2026 12:11:17	BUILD SUCCESSFUL in 1m 9s
build	04-Mar-2026 12:11:17	2 actionable tasks: 2 executed
simple	04-Mar-2026 12:11:17	Finished task 'Clover Report' with result: Success
simple	04-Mar-2026 12:11:17	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	04-Mar-2026 12:11:17	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1...
simple	04-Mar-2026 12:11:17	Finished task 'TestNG Parser' with result: Success
simple	04-Mar-2026 12:11:17	Running post build plugin 'NCover Results Collector'
simple	04-Mar-2026 12:11:17	Running post build plugin 'Artifact Copier'
simple	04-Mar-2026 12:11:17	Publishing an artifact: Clover Report (System)
simple	04-Mar-2026 12:11:19	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.924 s
simple	04-Mar-2026 12:11:19	Publishing an artifact: TestNG report
error	04-Mar-2026 12:11:19	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/test does not exist.
simple	04-Mar-2026 12:11:19	The artifact hasn't been successfully published after 2.170 ms
simple	04-Mar-2026 12:11:19	Running post build plugin 'Artifactory Release Management Staging'
simple	04-Mar-2026 12:11:19	Running post build plugin 'Artifactory Build Info Copier'
simple	04-Mar-2026 12:11:19	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	04-Mar-2026 12:11:19	Running post build plugin 'npm Cache Cleanup'
simple	04-Mar-2026 12:11:19	Running post build plugin 'Clover Results Collector'
simple	04-Mar-2026 12:11:19	Running post build plugin 'Docker Container Cleanup'
simple	04-Mar-2026 12:11:19	Finalising the build...
simple	04-Mar-2026 12:11:19	Stopping timer.
simple	04-Mar-2026 12:11:19	Build JB-GDB744-JOB1-5 completed.
simple	04-Mar-2026 12:11:19	Running on server: post build plugin 'NCover Results Collector'
simple	04-Mar-2026 12:11:19	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	04-Mar-2026 12:11:19	Running on server: post build plugin 'Clover Delta Calculator'
simple	04-Mar-2026 12:11:19	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	04-Mar-2026 12:11:19	All post build plugins have finished
simple	04-Mar-2026 12:11:19	Generating build results summary...
simple	04-Mar-2026 12:11:20	Saving build results to disk...
simple	04-Mar-2026 12:11:20	Logging substituted variables...
simple	04-Mar-2026 12:11:20	Indexing build results...
simple	04-Mar-2026 12:11:20	Finished building JB-GDB744-JOB1-5.